Differences
by Kale
Summary: Discontinued, possibly being adopted by animefan669
1. There's No Place Like Home

Authors note: This story takes place in an AU. Shinji is brought to this AU when he busts out of the Twelfth Angel. It was mentioned in the series that the Angel might be connected to another universe and I decided to explore this idea. Differences 

By Kale

Proofreading by The Master Chief

* * *

Chapter 01

Shinji looked at the clock on his watch, and then lay back against the chair of the entry plug. It seemed like forever since the Twelfth Angel had swallowed him and his Evangelion whole. He brought the Eva out of life support mode just long enough for a display, but was only greeted with white nothingness, then switched the Eva back into life support mode and lay back against the seat. Shinji just looked around within the dimly lit entry plug. 

_The LCL is getting cloudy, _Shinji thought. _The filtering system must be shutting down. The Smell of blood is getting stronger... _He jumped out of his seat and desperately tried to open the hatch, but the tough steel wouldn't even budge. 

"Let me out! Misato! Asuka! Ayanami! Dr. Akagi! Father!" Shinji slammed his fists repeatedly against the hatch, but to no avail. He then slumped down in his chair and began crying as hope quickly left him. "Please… someone help me." Shinji laid his head and arms against the controls of the Eva. Shinji soon cried himself to sleep.

Shinji woke up some time later and checked his watch. He was already near the sixteen hour limit, but he could have figured that out without the watch: the LCL had already become even cloudier and it was becoming harder to breathe. _I guess this is the end._ Shinji thought despairingly just before he blacked out.

* * *

A shadow had swallowed a large portion of the city, a large black and white striped sphere at the center of it, which was slowly making its way to the Geofront. With its designation as the Twelfth Angel, Units Zero and Two were positioned near the edge of the shadow. Asuka was about to take a shot at the sphere with the large pistol in her Eva's hands when the ground began to shake violently.

On the bridge in Central Dogma, confusion reigned supreme. "What the hell is going on?" Misato demanded.

"I can't figure it out!" Makoto replied, his voice straining to hide his frustration. 

"All readings are going off the scale!" Maya reported.

"But..." Ritsuko protested. "... We haven't even done anything yet!"

The bridge personnel watched as a metallic purple arm burst from the sphere, then another, the two arms pulling in opposite directions, prying the Angel open as blood poured from the gash. A head slowly poked its way out of the Angel; dark purple, with two angrily glowing eyes and a long horn atop its head.

Asuka stared at the scene in horror from within the safety of Unit Two. "I'm... I'm piloting a monster like that?" she whispered in dull shock to herself.

Soon, the Angel was ripped open, exploding in a gruesome shower of blood that showered anything and everything nearby. The shadow under it immediately vanished, revealing the city once again as a massive monstrosity resembling Evangelion Unit One stood proudly, roaring in rage before it powered down. The now powerless machine's eyes lost their glow, and the monster slumped forward, no longer active.

"What's the status of Unit One!?" Misato demanded.

Makoto quickly entered the appropriate commands into the terminal. "Unit One's still inside its cage!"

"Then what the hell is that!?" Misato shouted as she pointed to the screen, which displayed a creature that looked frighteningly like the aforementioned Evangelion.

"Send out a recovery team to retrieve the replica of Unit 01," Ritsuko commanded. She then sighed softly as she took a cigarette and lighter from her coat pocket and lit up, taking a nice long drag. _I wonder what Commander Ikari is going to think when he hears about another Unit 01,_ she thought worriedly. This was going to be a long day.

* * *

Recovery of Unit One went pretty much the way had always gone in the past after a berserk episode. However, **this** Unit One had to be stored inside one of the spare cages. Ritsuko and Misato stood along one of the nearby walkways, where they would get a good look at whomever it was piloting this Eva. They watched and waited with baited breath as the plug was ejected from the back hatch just behind the Eva's head. After being twisted out, the hatch opened. The two women gasped in shock at who they saw: Shinji Ikari.

"It's impossible..." Misato said numbly. "He's... He's **dead!**" She ran up to the plug.

"Misato!" Ritsuko shouted as she ran up after her. "Careful, we don't know who this really is!" She grabbed her friend's arm and pulled her away as a group of medics came. "Don't get too close to him!" Ritsuko then turned her attention to the people getting the boy out of the entry plug. "Keep him secured to that bed until we can ascertain who or what he is!" 

The boy's arms and legs were then securely strapped to the stretcher, and he was carted off to the infirmary.

* * *

Shinji groaned as he slowly regained consciousness, his head throbbing painfully as he slowly opened his eyes. He kept them half-open, trying to get used to the overly familiar ceiling and its sharp florescent light

_I'm still alive? _Shinji thought as he blinked a few times. _ But... How? _He tried to bring up his right hand to cover his eyes but it jerked back towards the bed. Confused, he looked over at his right hand, only to find it secured to the bed by a tough-looking strap of a tight, thick material. Looking at his left wrist, he found he was bound in a similar manner. He also noticed that the plug suit had not been removed.

"Why am I...?" Shinji softly began, confused by it all.

"Safety precaution."

Shinji sat up as best as he could and looked towards the other side of the room, where he saw his guardian. She had her arms crossed over her chest and wore a stern look on her face that suggested she wasn't in the best of moods.

"Misato..." Shinji said faintly, blinking in confusion as he stared helplessly at her.

She stepped toward the bed and looked down at him. "Who are you?" She demanded.

Shinji looked at her in obvious bewilderment. "You... You don't know me..?"

"I know who you look like, not who you are. Now tell me who you are."

"It's me, Shinji."

"Impossible," she shot back. "He's dead."

"What do you mean dead?"

"He died a few months back," Misato replied, her voice sounding a bit shaky. "He didn't survive an attack from the Fifth Angel."

Shinji blinked several times as Misato's words sunk in. He remembered what had happened when he was first sent out to face the Fifth Angel. It had blasted right through the chest of Unit One, and thus him, leaving him unconscious for several hours. That he was even alive right now was thanks to Misato's quick thinking in ordering the retraction of his Evangelion before he was completely toasted. _Not something I'd want to experience again,_ Shinji thought with a nervous gulp.

A small cough from Misato brought him back to reality. "I'm going to ask you one more time," she said sternly. "Who **are** you?"

Shinji opened his mouth to respond, but was interrupted when the door opened and Dr. Ritsuko Akagi walked in. "That's **enough**, Misato," Ritsuko chided her old friend. "Shinji's been through enough without you harassing him."

Misato turned and gave Ritsuko a sharp look. "Why are you calling him Shinji now? **You're** the one who said he might be anyone."

"Because that's exactly who he is," Ritsuko explained calmly. "At least that's what the DNA sample I took suggests. 100% match with our records. This is him, no doubt about it."

"Then how would you explain him being here when we both saw him die against the Fifth Angel?" Misato looked at the blonde as though she had lost her mind.

"Your guess is as good as mine." Ritsuko shrugged as she looked at Shinji, the boy giving her a blank look in turn. "There's still so much about the Angels we don't understand..."

Shinji had been listening to the conversation the entire time, though it wasn't helping him any. _This is crazy, _Shinji thought. _ How could Misato think I died so long ago..? What **other** surprises are going to welcome me? _

Shinji decided that he wasn't going to get any answers laying on this bed. "Excuse me, I don't mean to interrupt," he began, "but can you please let me go?" 

Misato looked at Shinji and then at Ritsuko, who nodded at her friend. "I don't see why not," she told the Major with a smile.

Misato walked over to Shinji and undid the straps holding him to the bed. Shinji began rubbing his wrists; they were quite sore from straining against the hard material. "I'm sorry..." She began, her eyes welling up with tears before she started sniffling, rubbing her eyes as they clouded with tears. 

"Um, it's okay, Misato..." Shinji assured her, flashing her a warm smile.

"You should take him back to your apartment," Ritsuko suggested in a soothing tone as she patted Misato on the shoulder. "It'll do you both some good."

"What about Asuka?" Misato asked, sounding more uncertain than anything else. 

"That," Ritsuko shot back with a soft smile, "is your problem."

"Gee, thanks," Misato sarcastically replied. With that, Ritsuko gave Misato one last reassuring smile and exited the room, leaving them alone.

"Um..." Shinji looked down at himself as he got off the bed. "I'd really like to change..."

Misato turned back to Shinji, blinking as she realized the situation. With him dead for so long, the lack of a male pilot meant that no boys' clothes were immediately available. "We're gonna have to wait till we get home," Misato told him, biting her lower lip as she did. "We don't have anything you can put on here..." 

Shinji nodded. "All right," he said with a nervous smile.

Misato motioned for Shinji to follow her. He did as he was told, walking with her through the hospital, though he didn't feel entirely comfortable walking around in his plug suit. He waited till they were in the parking garage until he said anything. "Um, Misato..." Shinji gulped nervously as he tried to speak. "Can I ask you something?"

"Sure, as soon as we get in the car," Misato replied. Her voice was considerably softer and more insecure than he was used to, as though she had no idea what to say to him.

Shinji walked at Misato's side through the rows of cars, paying little attention to where he was going as he compiled a list of questions in his mind. All the cars looked the same to him, anyhow.

"Aren't you going to get in?" Misato's voice suddenly shook him out of his deep thoughts.

Shinji blinked and looked up, seeing Misato's blue sports car before him. He walked up to the car, blushing as he opened the passenger seat. "S-sorry..." He stammered, biting his lower lip as he climbed in and looked on ahead, sitting there nervously. _Maybe I should wait till we get home,_ Shinji thought, trying to relax as Misato backed out of her parking spot and drove off. It would be nice to be home.

* * *

Shinji and Misato walked up to the door of the Katsuragi apartment. Fishing for her keys, Misato looked over to Shinji with a soft smile, though her eyes betrayed her heavy heart. "Shinji?" she asked carefully. "Could you please wait here? I... I have to talk to Asuka alone for a bit..."

_I wonder what the big deal is?_ Shinji thought as he looked dumbly at her. _She wasn't even here when the Fifth Angel came. If I died then, how could she know me at all?_ Resigning himself to the fact that he really didn't know anything anymore, he just shrugged, smiled, and nodded. "Okay," he told her. "I'll wait here."

* * *

Misato opened the door and then closed it behind her, wanting to make sure she talked to Asuka before she saw her guest. "I'm home!" she shouted, trying to sound as normal as she could. She found Asuka in the living room, staring blankly at the TV. She was wearing a boy's white buttoned shirt and black slacks, as she'd dressed almost every day since Shinji died.

"Hi there, Misato," Asuka replied lifelessly. The girl was still suffering even today.

"Say, Asuka..." Misato began, pausing as she tried to figure out how to talk to her. She took a deep breath she resumed. "We're having someone staying with us for a while..."

"Guy?" Asuka said, her voice taking on an accusing tone.

"Um, yeah..." Misato fidgeted nervously, already feeling uncomfortable with her charge's reaction.

"Keep him out of Shinji's room," Asuka replied, her voice starting to crack slightly.

Misato sighed, knowing that simply wasn't going to be possible. "I don't think we'll be able to..."

"What!?" Asuka shot back as she looked over as Misato in rage. "You... You wouldn't..." The girl's eyes were red, and her face was streaked with small lines of water. _Crying again..._ Misato thought, looking away from her with a heartfelt sigh. _What if this hurts her more...?_ "Please," Asuka continued, trembling as she stared at her. "You promised you'd leave Shinji's room alone..."

Misato shifted uncomfortably, unable to keep her cool under the penetrating gaze of those grief-stricken eyes. "It's a bit hard to explain, but... He's standing outside the apartment door."

Asuka glared hatefully at her guardian for a moment, getting up on her feet as she did. "I swear, if you're trying to introduce me to someone else...!" With that, she marched past Misato, heading for the door.

"Asuka, wait!" Misato called after her, but Asuka was already at the door.

* * *

Shinji stood at the door, with only his thoughts to accompany him. _Why would Misato want to talk to Asuka before letting me in?_ He thought, clearly confused. _Why would it matter anyway? It's not like she ever cared about me._ Shinji shrugged to himself as he stood there, waiting silently for Misato's little talk to finish.

The door suddenly hissed open, bringing Shinji out of his little train of thought. "Gee, you don't need to get me all startled Mi..." The rest of the word vanished from his lips as he looked up at the doorway. Instead of Misato, he saw a fire-haired beauty with sad looking blue eyes staring back at him, dressed in his own shirt and pants. As he looked on in surprise, her expression changed before him; her eyes widened, her mouth opened slightly, her body trembled slightly before him.

"Shinji..." Her voice sounded faint, full of wonder and shock as she stepped closer to him. Her eyes were welling up with tears as she gazed at the shocked Shinji, who stood there helplessly, powerless to do anything but watch as Asuka gazed at him with those big blue eyes. She suddenly leapt at him, her arms wrapping around his back as she started showering his face with kisses, holding him harder than he'd ever been held before. "**Shinji!**"

End Chapter 01 


	2. Home Sweet Home

Differences

By Kale

Proofreading by The Master Chief

* * *

**Chapter 02**

Shinji stood dumbfounded in Asuka's arms, blinking several times in shock. Okay, I'm missing something here, Shinji thought to himself in a daze as Asuka barraged his face with kisses. _Just **why** is she acting this way? _ So overcome was he that he didn't even notice Misato walk up behind Asuka and tap her shoulder.

"Whoa there, Asuka!" Misato teased, "Why not let him breathe a bit? And it'll be hard for him to get out of that plug suit while he's wearing you at the same time."

Asuka blushed and released Shinji, holding her arms behind her back as she took a good look at him. Indeed, he stood there in his plug suit, a rosy shade of red covering his cheeks. She giggled softly and looked down slightly, blushing in embarrassment from her outburst.

Misato gave Shinji a warm smile and a not. "You'd better take a bath," Misato advised, quickly adding "I'll get you a change of clothes, so don't worry."

Shinji nodded slowly and walked past the two girls and into the house, looking around cautiously as he made his way toward the bath. At least the apartment looked like it had for the most part. There was some blessing in that.

* * *

Asuka sighed softly as Shinji made his way into the apartment, her eyes glistening as she slowly turned around to follow him. "Shinji, wait—"

Misato blocked her with her forearm and gave her a hard look. "You might want to tone down the lovey dovey act, Asuka," she admonished the redhead.

Asuka gave Misato a puzzled look for a moment, then pouted at her. "Why?" she asked, her voice a bit whinier than normal.

Misato paused and closed her eyes a bit, then sighed and looked down at Asuka, her eyes heavy and weary as she spoke in gentle, hushed tones. "We both saw Shinji die..." She began, forcing out the words as she saw the tears start to well up in Asuka's eyes. "I can still remember Shinji leaping in front of you to shield you trom the 5th Angel's blast..."

"It's not like I forgot!" Asuka shouted bitingly. "But, he's right there..."

"I know he looks like Shinji, but..." Misato sighed again. "It's just, how can he possibly be here if he's dead...? Even Ritsuko says it's him, but..."

"Well I don't care why! He's here **now**, and that's all that matters to me!" With that, Asuka marched past Misato, her long red hair flipping about wildly behind her.

"He seems different somehow…" Misato whispered to herself as she walked back into her apartment. "I just hope he doesn't hurt her again..."

* * *

After making sure the apartment was still the same, which was at least some comfort, Shinji stopped in front of the bathroom door. _I know she said she'd get me some clothes..._ Shinji thought, _but I really should do that myself. I don't want burden anyone._ He walked away from the door and headed over to his room, opening the door slowly. The sight was perhaps one of the most amazing and shocking in all his life. His sleeping mat was perfectly laid out in the center of the room, with an entertainment center comprised of a television, DVD player and several games consoles. On the left wall was a fine oaken desk upon which a desktop computer sat, two neat stacks of SDAT cassettes sitting next to the monitor. The whole setup looked rather clean, no dust or anything. It didn't look like anyone had even been in this room, save for someone to keep dust and insects away. _Whoa.... This stuff isn't mine..._ Shinji mused in amazement as her shook his head and looked at the dresser at the right end of the room. _What** is** all this?_ He quickly found a pair of black pants and a white button-up shirt, then closed the drawer and immediately headed to the bathroom.

Once in front of the bathroom again, Shinji knocked once to make sure it was safe. The silence was reassurance enough, and he opened the door and walked in, sliding it closed again behind him. Quickly setting his chance of clothes atop the sink, he removed his plugsuit and turned on the water, looking at the water slowly rising in the tub. When the water was finally up to his liking, he turned the faucets off and slid into the tub, sighing to himself as he relaxed, the warm water relaxing his tired muscles. He took this moment to run a checklist of everything that was abnormal. First, he was supposed to be dead. Not something people just forget in passing. Then, there was Asuka, dressed in a shirt and pants like he normally wears, smothering his face with kisses while trying to snuggle the life out of him. He shrugged and let out a sigh, giving up hope on figuring out anything anymore, gazing up at the ceiling as he relaxed in the tub.

"At least some things never change..." he murmured to himself as he gazed at the ceiling.

* * *

Asuka and Misato were sitting in the living room, watching TV when Shinji entered the living room, wearing a black pair of pants and a buttoned up white dress shirt, as he had always dressed. He took another look at Asuka, dressed in exactly the same manner, and shivered. Of all the things that had changed, this was perhaps the most unsettling.

Misato turned herself around from her spot on the floor to face Shinji. "Hey Shinji," she said warmly, "You hungry?"

Shinji put his hand to his stomach as it let out a small rumble, then smiled sheepishly and nodded. "I guess I am" he replied, a bit of a blush forming on his cheeks. "I'll start dinner."

Misato cocked her head to the side and looked at Shinji. "Since when do you cook Shinji?" The question didn't sound mocking or joking at all to Shinji's ear, but rather carried the tone of genuine confusion, which only served to confuse Shinji more. 

He decided to take her to task on it, just in case. "Huh? What do you mean? I've always cooked since I came here." _She knows that, _Shinji thought to himself as soon as the last word left his lips.

Misato stood up from her seat on the couch. "Don't worry about it, I'll cook."

Hearing Misato offer to cook immediately set off more than a few bells of warning in Shinji's head. Before speaking, he looked over at Asuka, expecting some sort of reaction to Misato's announcement. Surprisingly, the redhead didn't react and continued to watch the TV.

Shinji looked back at Misato. "Are you sure?" he asked, making a last ditch effort to try and dissuade Misato from cooking. 

Misato would not be denied. "I'm sure, now why don't you go watch TV with Asuka while I fix dinner?" The tone was kindly, but with just enough edge to suggest it was more than a request.

_Once her mind is made up, there is no stopping her. _Shinji thought. "Ok, I guess," he sighed with a shrug, praying silently to the gods that it would at least be edible.

While Misato made her way into the kitchen to start dinner, Shinji made his way to the couch in front of the television, plopping down on the opposite end from where Asuka was sitting. Tension permeated the air as the two youths shared an awkward silence as they sat there, silently watching a commercial for some new videogame. Shinji couldn't get over what had happened in the doorway earlier, and couldn't even begin to come up with anything to say. Instead, he simply sat there, staring at the screen.

* * *

Asuka looked at the television, but barely paid attention as the show she'd been watching came back from commercial. Her eyes kept darting back over to Shinji, who looked uncomfortable and out of place. _Why's he so fidgety? _Asuka wondered to herself. _It couldn't have been because of the kisses at the door._ Asuka sighed and shrugged, then smiled halfheartedly._ There is one way to find out, I guess._ However, as Asuka opened her mouth to break the silence, Misato walked into the living room. "Hey guys, what's with the silence? Getting' a little cozy?" Misato teased. "Anyway dinner's ready."

With that statement, both teens stood up off the couch and made their way to the dinner table. Asuka looked over at Shinji as he walked with her, and couldn't quite get past the look of dread in his eyes. _What's **with** him?!_ Asuka pondered. _You'd think Misato was a bad cook or something..._

* * *

After the table was set and everyone sat down, Shinji warily took a bite of the steak in front of him, barely noticing that Misato's dinner at least looked better than normal. _Wow, this is pretty good. _Shinji thought as he looked at Misato. 

"Very nice, Misato," Shinji said with a smile. "When did you learn to cook so well? "

Misato finished chewing the food in her mouth and swallowed. She then took a quick chug out of her can of beer before answering, "Huh? What do you mean Shinji?"

_ At least that's still the same, _Shinji thought, looking at the can of Yebisu for a second before looking back up at her eyes. "You've just never cooked so well before," he replied.

Misato and Asuka shared a quick, confused glance. "You've always said I cooked well Shinji," Misato said softly.

Shinji had no reply to that. _There is definitely something weird going on here, _he thought, biting his lower lip as he did..

The 'family' ate the rest of their dinner in an uneasy silence. Surprisingly, Shinji was the first one to finish his dinner. He stood up and took his dishes to the kitchen where he deposited them in the sink. He then walked back into the dinning room. "Well, I'm going to head to bed. I'm a bit tired, and tomorrow's Monday."

"Ah... About school, Shinji..." Misato began, knowing what Shinji meant but not knowing the best way to say what she had to. "Maybe you should wait a couple of days."

Shinji looked at Misato and blinked in surprise. "Why would I do that?" he asked.

"Well…lets just say that it might be a bit awkward." 

Shinji shrugged. Not like it would have been the first time.

"Besides, I need to talk to you tomorrow."

Shinji nodded, "All right, then. Good night Misato, good night Asuka."

"Good night Shinji" They replied.

Shinji then walked off to his bedroom, pondering the oddity of the whole day.

* * *

With Shinji out of the way for the moment, Misato turned her attention to Asuka. "**Now** do you understand why I told you to tone it down?"

"A little" Asuka replied. "He seems so different.... I know he's Shinji, but the way he acts..."

_She isn't speaking in that monotone voice anymore, _Misato thought, relieved to hear emotion in the girl's voice for the first time in seemingly an eternity. "Maybe he just doesn't remember certain things." Misato offered. "I can't imagine it's been easy for him."

"So... What should we do?" Asuka asked, her voice shaking slightly.

"I don't know, really," Misato admitted. "All I can do is talk to him, ask him about what he remembers, what he doesn't. You can do the same when you get home from school." Misato sighed a bit and put a hand on Asuka's shoulder. "Just... don't be too harsh with him, okay?" she pleaded with her redheaded charge.

Asuka nodded in agreement. "All right."

"We should turn in for the night as well," Misato told Asuka, yawning softly to emphasize how tired she was.

"Okay then," Asuka chirped as she nodded in agreement. "Good night, Misato."

"Good night, Asuka." 

With that, both women stood up from their seats at the table and made their way to their bedrooms. Asuka paused in front of her room. She turned around and looked at the door with the familiar sign marked with the text 'Shinji's lovely suite'. _Good night my Shinj, _Asuka thought. Asuka then turned around, opened her door, stepped through and slid it shut behind her.

* * *

**End Chapter 02**

* * *

Author

What do you think? Both MC and I have been having writing troubles, and various other things have been going on. Such is the way of things. Anyway, don't forget to leave comments, as they're always necessary. Here's to hoping the next chapter comes out soon. See ya!

Proofreader

No, I have not abandoned Duke Nukem: Tokyo-3 Project. I'm just having a bit more trouble with Chapter 5 than I thought. Anyway, I'd like to thank Kale for sending this in to be proofread. I needed to think of something other than action, it might help loosen me up. I've seen him improve as a writer, and my work has gotten more and more easy since then. I look foreward to the day when both of us don't need much proofing in our works – keep it up, Kale, you're getting closer to being one of the better writers here. Anyway, feel free to send comments to Kale about the work. Unfortunately, I don't have a free email to send stuff to atm, as MasterChief@disc13.com doesn't work anymore (Sorry about the initial troubles getting the fic, Kale.) Anyway, I'd better quit rambling on. See ya soon.


	3. Suprises

Differences

By Kale

Proofreading by The Master Chief

* * *

**Chapter 03**

Misato's habitual morning beer yell yanked Shinji cruelly from his sleep. _Some things never change, _he thought with a smile. Not wanting to get up quite yet, he lay there and stared up at the ceiling. _The ceiling is all that's familiar to me here. There is way too much stuff in this room. _ He took another survey of the room, still in disbelief of how many things 'he' possessed. 

Turning his attention to the sounds outside the room, he caught Misato and Asuka's voices. He couldn't quite make out what they were saying, but caught a couple of words – Though certainly not enough to make out the topic of conversation. After a while, Shinji managed to hear Asuka and Misato say their goodbyes before the former went off to school. He then returned to silent contemplation. _ I can't stay in bed all day, _Shinji thought, _Misato said she wanted to talk to me today. _ Shinji threw his blanket aside and got up, then walked over to his closest. He opened the door, once again finding clothes in his closet that he wasn't used to seeing, and grabbed his school uniform, feeling more comfortable with his regular white dress shirt and black pants than in anything else that he saw. 

Shinji quickly got dressed, and then exited his room, sliding the door shut once again behind him as he made his way to the living room area. _I guess it's time to find out what Misato wanted to talk to me about. _ He couldn't imagine anything good could come out of it.

* * *

Misato sat the table eating her "traditional" Japanese breakfast, shoving her food down her throat and taking deep swigs of her beer to wash it all down. Putting her beer can down, she saw Shinji standing in front of her and the table.

"Good morning Shinji," she said cheerfully.

"Good morning Misato," Shinji replied in a soft, hesitant voice.

Misato made a motion for Shinji to sit down. "I made breakfast, but it may a little cold since you decided to sleep so late," she said with a wink. 

"Thanks Misato," Shinji said as he pulled a chair out so he could sit down, "but I'm not really hungry." He then sat down in the chair, directly across from Misato at the table. "You said you wanted to talk to me about something, Misato?"

Misato took one last swig of her morning beer before setting it down on the table and looking at Shinji, her eyes betraying the serious nature of what was on her mind. "The first thing I want to talk to you about is about your going back to school. I'll need to check with the commander before you can do that."

Shinji blinked in confusion for a moment and then responded. "Why would you have to check with the _commander?_"

Misato couldn't help but notice how resentful her charge seemed, but continued anyway, her voice slightly hesitant. "Most of the school attended your funeral, Shinji. She might have concerns about you going back, all that considering." 

"I suppose that would be a good reason to check with the commander" Shinji answered, looking more than slightly confused by Misato's words. _What does she mean she will have to check with "her"?_ Shinji sighed softly, wondering what, if anything, had happened to his father, but not really able to bring it up.

"But that's not the only reason why I wanted to talk to you today," Misato continued. "I want to ask you some questions if it's ok with you."

_Questions? About what? _ Shinji thought before shrugging. "Ok, go ahead."

Misato cleared her throat. "Do you remember how you met Asuka?"

"Of course, how could I forget? We picked her up on Over The Rainbow." Shinji blushed softly at the memory. To this day, he wondered what was worse; Asuka's attitude or the joking remarks his friends made about him in her plug suit.

Misato opened her mouth to reply when the phone rang. She pushed her chair back from the table and stood up. "I'll be right back." 

Shinji nodded, "alright".

She then walked out of sight behind a door. Shinji listened closely as Misato spoke on the phone. 

"Hello, Katsuragi residence."

Silence for a few moments. Not long, but as anxious as Shinji was, it seemed like an eternity.

"Alright, I'll be down in a few minutes." After that, she walked back over to the table, looking somewhat disappointed.

"I was just called into work, so we have to talk later. I'll let you know later tonight if the commander says it's all right for you to go back to school. So now if you will excuse me, I need to get ready for work."

"Ok Misato, have a good day at work." After Misato left the dinning room to go change, Shinji stood up and made his way over to the couch. He flipped on the TV to see what was on early in the morning, looking more for anything to distract him than anything else.

* * *

Asuka, dressed in a girls' sailor-style school uniform, was making way across the schoolyard when she heard a familiar voice cry out for her to wait up. Asuka turned and waited for her best friend, as Hikari ran towards Asuka. Hikari slowed down to a stop, right next to Asuka, then bent over with her hands on her knees, trying to catch her breath. After a few moments, she straightened up and turned to face Asuka. "So how are you today Asuka?"

Asuka smiled slightly. "Better than I've been in a long time," she chirped.

Hikari noticed a hint of sadness in Asuka's eyes, but also saw that she wore a small smile and that she wasn't dressed in the boys' school uniform like she had been doing ever since Shinji died. She smiled, "That's great. Can I ask why?"

Asuka was beside herself. As much as she wanted to tell her best friend that Shinji was alive, she didn't know if she would believe her. "I can't say right now."

Hikari put on a mock-disappointed face. "Aw come on. You can tell me. I'm your best friend! If you can't tell me then who can you tell?"

Asuka looked around, aware of the students in the schoolyard. "I can't say with so many people around. I'll tell you more after school when we are alone."

Hikari jokingly pouted for a minute. "Oh fine! Be that way then." She adopted a tone more fitting to her status as class representative. "We had better be going. I don't want to be late for class. It wouldn't be good for the class representative to be late to class, after all."

Asuka nodded, "alright." The two then made their way towards the school.

* * *

Deep in the bowels of the Geo-front, Misato entered the commander's office and walked up to the desk. "Major Katsuragi, reporting as ordered," Misato said as she saluted the commander, then brought her arms down against her sides. She stood before a large, polished oak desk with the chair turned away from her. With only the desk and some electronic equipment, the room seemed somewhat bare, but Misato had gotten used to it, having come here many a time. 

"Give your report," The commander ordered.

Misato gulped hard, dreading this very moment. _May as well get it over with,_ Misato thought as she cleared her throat. "Soon after the Evas got into position to commence the operation to defeat the 12th Angel, the ground began to shake violently. Shortly after, the angel's body began to rip open, and a deafening roar filled the air. One gigantic purple hand forced it's way out of the tear, then another, and slowly they began to force the opening wider and wider until the Angel finally exploded, covering anything in the immediate vicinity with blood. Something that looked like Unit 01 emerged from the bloody body. I can tell you for sure it wasn't ours."

The commander turned around to face Misato, her eyes cool and focused. "How can you be so sure?"

Misato nodded, "I had Hyuuga check the status of Unit 01 and he confirmed it to be still in its cage."

The commander turned back away, staring off into nowhere. "Interesting," she breathed. "Was there anyone piloting this Unit 01?"

"Yes."

The commander paused a moment before speaking again. "Do you know who the person is?"

Growing increasingly uncomfortable, Misato responded. "It appears to be Shinji Ikari, commander."

"I'm glad we know who the pilot is…" The commander said. She shook her head, and then paused for a brief second, "I think I may have misheard you. Please repeat what you just said."

"The pilot was Shinji Ikari," Misato repeated, shuffling in place uneasily. "Dr. Akagi checked his DNA to be sure, and it's an exact match."

The commander stood up quickly and faced Misato, her eyes looming down on hers imposingly. "Where is this 'Shinji Ikari' right now?"

"Back in my apartment, but why--" Misato was suddenly cut off as the commander raised her hand.

"Take me to your apartment, I wish to see him for myself."

Misato saluted, "Yes commander, follow me please."

With that said, Misato led Commander Yui Ikari out of the office. A million thoughts were running through her mind at the moment. She thought back to Shinji's resentful voice before. Would he react poorly to seeing her now? _They were so close…_ Misato recalled. _I really don't want to see Shinji or Commander Ikari hurt…_ Misato sighed, trying to think of a positive outcome as she led the commander through the halls of Nerv to the parking area.

* * *

The day seemed like it would never be over for Asuka as she listened to the teacher go into his daily rambling about 3rd Impact. It seemed as though an eternity had passed before the bell finally rang, signaling everyone in the class to file out, including the teacher. Soon, only Asuka and Hikari remained in the room, sitting next to each other. Hikari packed her bag and looked over at Asuka, who was doing the same, then tapped her friend's right shoulder. "So what's the big secret Asuka?"

Asuka glanced around the room to make sure no one was in hearing range. Then in a whispered voice she said to Hikari, "Shinji's alive."

Hikari gasped, "No… He can't be…"

Asuka nodded, "I didn't think it was possible, but I saw him with my own two eyes. I touched him with my own two hands…" Asuka began breathing heavy, biting her lower lip, that single touch making her heart race as she remembered it.

Hikari looked at Asuka with a worried gaze. "Are you sure you're ok? I mean we both saw him in the casket at the viewing. We saw him buried… I don't think I'll ever forget how hard you took it, how much you cried..."

At the mention of Shinji's death, Asuka eyes welled up with tears a little. She then narrowed her eyes, her face hardening into a look of determination. _I'm not going to cry again…_ She thought. Aloud, she said, "Fine, if you don't believe me, then you leave me no choice. Come with me, we're going to my apartment and I'll show you."

Asuka just grabbed Hikari's right wrist and almost dragged her out of the classroom, ignoring the class rep's protests. _Just you wait, Hikari…_ Asuka thought, looking ahead. _You'll see… _

* * *

Authors note: I apologize to my readers for not updating sooner. I plan on writing more and trying to update sooner than I have been. Hope you enjoyed the chapter.

* * *

A message from the proofreader.

I'd like to make an apology to Kale, the author. I had put this off for way too long for way too many subpar reasons. I did him a massive disservice, and for that, I'm sorry. I don't know if he'll have me, but I really do want to continue to proofread this series, and I promise that I'll be faster about it if given the chance. Again, I apologize, and hope to continue my work.

The Master Chief.


	4. Reunion

Differences

By Kale

Editing by The Master Chief

* * *

**Chapter 04**

Shinji turned off the TV, which was currently showing another dull news program, and set the remote down on the couch.

_ There's never anything good on nowadays, _Shinji thought as he rose from his position on the couch to stretch his arms and legs. He'd been sitting on the couch since Misato left to go to work, getting up only to grab a snack or go to the bathroom. After stretching, Shinji started surveying the apartment trying to find anything that would break the choking monotony. Eventually he noticed something or more specifically the lack of something that piqued his interest.

_ That's odd, _Shinji thought._ Pen Pen's refrigerator isn't in its usual place. I wonder where Misato keeps him. I'll have to ask her the next time I see her. _Shinji's gaze turned to the clock on the wall above the TV. Asuka wouldn't be back from school for several hours yet. He'd almost lost hope on finding something to do with a thought suddenly struck him. _I wonder if my cello is in the closet where I usually keep it._

With that in mind, Shinji made his way through the apartment and into his room. He slid the closet door open and was once again bombarded with the sight of bright and unfamiliar clothing. Shinji started pushing clothes out of the way and began searching through the closet. As he worked his way toward the back, he noticed what appeared to be the top end of his cello case. Shinji grabbed it and pulled it out of the closet, relieved to find it was indeed a cello case and not something else. _Finally, _Shinji thought, _something that is familiar besides the ceiling._

Shinji laid the case on the ground, undid the snaps and opened the case up. _Exactly as I remembered it, _Shinji thought fondly, _although it looks like it hasn't been opened in a while_. Shinji pulled the chair from his desk to the spot in front of the instrument case. He sat down in the chair and opened it, then slowly and carefully lifted the cello out. He set it down it front of him and played a test note. _It sounds like it needs to be tuned, _Shinji thought, _thankfully my teacher taught me how to take care of it as well as play it. _Shinji then proceeded to tune the cello by playing test notes and tweaking the cello until the musical notes sound perfect to his ears.

Shinji began playing the first of the many songs he learned from his teacher. He soon became absorbed in the sound of the music and lost track of the world around him.

* * *

Asuka and Hikari walked out of the apartment building's elevator. They walked in silence down the dull, gray painted hallway at brisk pace towards Misato's apartment. Asuka walked in front with Hikari trailing behind her. Hikari noted to herself that Asuka seemed as if she had something to prove. She also seemed to be more like how she was before Shinji's death.

Asuka froze in place in front of Misato's apartment door, almost causing Hikari to crash into her from behind. "Asuka please, give me some warning next time." Hikari complained.

Asuka turned around to face Hikari, a sheepish grin on her face, "Sorry."

She then assumed a solemn look on her face. "Hikari, I don't know how Misato will react once she finds out I did this without her permission but I need you to promise me that you will not speak a word of this to anyone. Not even your own family," she pleaded, almost sounding as if she were begging. Hikari nodded silently and smiles reassuringly as she replied. "Asuka, you have nothing to worry about," she said gently. "I'm your best friend remember? If you can't show me, then who can you show?"

Asuka, now reassured that Hikari wouldn't tell, nodded. "Thank you Hikari," she said, sighing in relief

Having sworn Hikari to silence, Asuka turned around and unlocked the door to the apartment, and led Hikari inside. As they entered the apartment, they were greeted with the sound of music. It was a song with a slightly melancholy tone to it. The music loudened as they ventured into the apartment. In the dining room, Asuka oriented on the origin of the music and determined that it was coming from Shinji's room. It was obvious to her already since Shinji was the only one, beside herself of course, that played an instrument in the apartment. Misato was way too clumsy to play an instrument _I always knew he could play, but I didn't know that he could play this well_, Asuka thought in amazement as she lead Hikari in the direction of Shinji's room.

Finally they arrived in front of the door to Shinji's room. Asuka put a finger in front of her mouth to signal for Hikari to be quiet. Asuka slowly and quietly opened the door so that she and Hikari could see inside. They were greeted with the sight of the back of a young man, in a school uniform no less, sitting in a chair playing a cello. Shinji seemed to be lost in his own little world.

"See Hikari? I told you he was alive." Asuka gloated in a whispered voice. No response came from her friend. "Hikari?" Asuka turned to face her best friend. Hikari was covering her mouth with her hand, her eyes bugged out in shock. Asuka shook her slightly. "Come on Hikari, snap out it." Asuka whispered. Hikari seemed to recover for a moment and then abruptly fainted, landing with a loud thud on the floor.

Shinji stopped playing, lowering the cello as he turned around to see what caused the noise. He found Asuka standing outside his room with Hikari on the floor seemingly unconscious. "Asuka, what is going on?" Shinji queried.

"No time for that Shinji. Help me move her to the couch." Asuka replied.

Shinji just nodded and moved over to where Hikari was. He grabbed Hikari's legs, making sure he looked to the side, while Asuka grabbed the upper body. Together they lifted Hikari and slowly brought her over to the couch. After they set Hikari down on the couch and put a pillow under her head, they faced each other.

Shinji spoke first. "So, um, what now?" Shinji asked while rubbing the back of his head.

"We do the only thing we can do, wait for her to wake up." Asuka replied. Asuka then grabbed the remote off the couch, turned on the TV, then sat down on the floor. Shinji shrugged and followed suit. They started to watch the TV as they waited for Hikari to wake up.

* * *

Misato and Commander Yui exited the elevator. It had taken longer then usual for Misato to get back to the apartment complex, not only due to an extra workload that delayed the both of them, but because Misato had decided on a more conservative driving style with her superior in the car. As they walked down the hallway, Misato glanced over at the Commander through the corner of her eyes. The commander had a calm, reserved look on her face. It was a sight Misato had become used to seeing at the Geo Front since Shinji had died.

As they stopped in front of the door to the apartment, Misato started searching through her purse for her key while the Commander just waited patiently. "I know it's in here somewhere", Misato grumbled as she continued to rummage through her purse.

While Misato was looking through her purse, Yui stood patiently by the door, thinking to herself. _I don't see how it could possibly be him. I'll never be able to get the image of my only son lying in his casket. _Just thinking of the funeral brought back memories of the battle against the Fifth Angel and of the actual funeral itself. She started to become upset but she managed to hold onto her composure. _Normally I wouldn't doubt Major Katsuragi and Dr. Akagi, but this time... _

After emptying her purse of all its contents, Misato turned to the commander. "Well it appears I don't have my key with me," Misato said with a bit of embarrassment, "but considering what time it is now, someone should be home. I'll just ring the doorbell." The Commander just sighed as Misato rang the doorbell.

* * *

Back inside the apartment, Asuka and Shinji were still watching TV, Hikari dozing peacefully on the couch behind them. They heard the doorbell ring and looked at each other, confused.

"I wonder who that can be? Shinji asked.

"Don't worry about it, " Asuka said as she stood up from her position on the floor, "I'll go answer the door."

Shinji shrugged, "ok."

Asuka made her way to the door, leaving Shinji to watch the TV alone. Opening the door, she was greeted by the sight of Misato trying to put her makeup back in her purse while Commander Yui Ikari stood patiently beside her.

"What brings you here Commander?" Asuka asked quickly, surprised by the appearance of the Commander at her residence.

"I was informed of a certain situation by the major here." Yui replied, "May I come in?"

"Of course." Asuka consented as she stood to the side. With that Yui entered the apartment with Misato trailing behind her. As Yui continued further into the apartment, Asuka pulled Misato to the side.

"Why is the Commander here, Misato?" Asuka asked in a whisper as she leaned in close to Misato.

"I had to give a report on the situation with the second Unit 01." Misato explained. "When I told her the pilot was Shinji, she demanded that I bring her here."

"She'll be glad to see Shinji as much, if not more, as I was." Asuka said.

"I'm not so sure of that." Misato responded with a dubious tone to her voice.

Asuka's face changed to a look of mild confusion. "Why is that?"

"When I was talking to Shinji this morning, when I mentioned the Commander he responded as if he resented her for some reason. Why he would resent her is what I don't know. I just hope things don't turn ugly."

* * *

While Asuka and Misato were talking amongst themselves, Yui entered the living room and froze in place at the sight before her; a young man in a school uniform looking very familiar. "It can't be…" Yui said in a soft, disbelieving voice as she rubbed her eyes as if trying to make the mirage going away. When she removed her hands from her face, the young man was still there. What she was seeing was no illusion. "Shinji!" She cried out to get his attention.

Shinji turned off the TV with the remote and stood up. He turned around to look at whoever called his name. It wasn't Hikari's, Asuka's, nor Misato's voice, that was for sure. What he saw was a brown haired, brown eyed woman who had a very familiar face and was tearing up. "Rei? No wait…" Shinji began. A vague memory began to surface from the deep recesses of Shinji's mind, a memory of holding out a cherry to a woman. That woman was his mother. "Mother…" Shinji began. Tears of joy began sliding down Shinji's cheeks. _I can't believe it's her._ Yui spread her arms wide for a hug and Shinji rushed over and leapt into her embrace.

Asuka and Misato poked their heads out from around a corner and saw the scene playing out in the living room. They looked at each other and smiled.

**End chapter 4.**


	5. Dialogue

Author's note: Yes it's official. Hell has frozen over. No your eyes are not deceiving you. This really was a new chapter in

my story and to top it all off, it was a longer chapter than I have written in the past. Sorry for the long wait.

Thank you to Dan01 and Zeroasalimit for pre-reading for me. Now onto the chapter.

Differences

By Kale

* * *

Disclaimer: I do not own Evangelion, any of its characters, concepts, etc or anything.

**Chapter 05**

While the joyous reunion between mother and son was going on, Hikari began to stir. As she continued to regain consciousness, she slowly opened her eyes. After completely gaining consciousness and her vision focusing, she found herself looking up at the ceiling. She surveyed her surroundings and found that she was on the couch in the living room. _How did I get here? _Hikari thought, _the last thing I remember seeing was Shinji sitting in his room playing his cello. But that's impossible. We all attended his open casket viewing and funeral._ She slowly raised herself into a kneeling position on the couch where she could look around the room. When she looked behind the couch, she saw Shinji and his mother hugging each other and crying tears of happiness. Hikari rubbed her eyes slightly and when what she thought was a hallucination did not disappear, she knew that her eyes were not deceiving her. _Asuka was right. I don't know how but Shinji is alive._

As she continued to watch the scene in front of her, she noticed Asuka and Misato peeking around a corner. When she made eye contact with Misato, Misato and Asuka quickly disappeared around the corner. Hikari continued to kneel on the couch, being careful to avoid being noticed, and watch in silence so that she did not disturb Shinji and his mother's reunion.

* * *

As Misato and Asuka pulled back from peeking around the corner, Misato quickly turned to Asuka.

"Why did you bring Hikari here? Misato asked Asuka sternly. "I told you that no one should know about Shinji until we know what the commander wants to do."

Unable to make eye contact with Misato, Asuka looked down at the floor and moved her right foot sheepishly back and forth on the floor "I'm sorry Misato," Asuka apologized, "During school Hikari kept bugging me. She wanted to know what caused the change in my mood. There was no way I could keep this from her. So I told her after school when no one else was around. When she said that it was impossible, I knew there was only one way I could convince her. I know I shouldn't have brought her here but I couldn't help myself. I told her that I would prove it to her by bringing her here, but I did have her promise that she wouldn't tell anyone, not even her own family."

"Look at me Asuka" Misato said firmly.

Asuka slowly raised her head and made eye contact with Misato.

Misato placed her right hand on Asuka's left shoulder and tried to be as reassuring as she could. "I understand how you feel about not being able to keep this from your best friend, but you have to realize that even we don't know how it is possible that Shinji is alive. Never mind the people in your school. I don't know if Hikari's promise to not tell anyone will be enough for the Commander."

"What will happen to Hikari then?" Asuka asked, afraid of the consequences her friend may face.

Misato gave Asuka a reassuring smile to try and assuage the red head's fears. "I don't think anything will happen to Hikari but we will just have to talk to the Commander. We'll cross that bridge when we come to it. Just promise me that you won't tell another soul about Shinji until the Commander gives the ok."

Asuka, with her fears pacified a little, nodded slowly, "I promise I won't tell anyone else."

"Now let's go see what we do about the situation." Asuka and Misato then proceeded to walk around the corner to join the others in the living room.

* * *

After releasing each other from their embrace, both Yui and Shinji wiped the tears of joy from their eyes so they could see clearly.

_I don't know how he's alive, but right now I don't care. He's standing here in front of me and that's all that matters, _Yui thought happily as she wiped the tears from her eyes.

"I've missed you so much these past few months Shinji" Yui said. "Losing your father was hard, but losing you was like everything I had in the world had been taken away from me."

Shinji's faced changed to a look of confusion. "What do you mean? What happened to father?"

Now it was Yui's turn to be confused. "You don't remember what happened in Germany?"

Shinji opened his mouth to respond but just then Asuka and Misato walked around the corner and into the living room.

"I hope we aren't interrupting anything important but there are some important matters to be discussed," Misato stated

Yui turned to face Misato. "Such as?" Yui inquired.

"Such as the presence of Miss Horaki on the couch" Misato said as she pointed directly at Hikari.

Yui turned to look where Misato was pointing and sure enough, there was Hikari on the couch kneeling. Turning back towards Misato and Asuka, Yui switched to her cool demeanor she used at NERV. "Why is she here?" Yui asked.

Shinji, becoming uncomfortable at the sudden change in his mother's demeanor and the sudden change of conversation, began to shift his feet nervously. He began to look around the room to find some reason to escape from the uncomfortable situation. Then the clock on the wall caught his attention and he noticed that it was almost dinner time. "I'm going to prepare dinner now," he announced breaking the uncomfortable silence. Using that as an excuse to get away, he made his way into the kitchen.

Asuka heard Shinji make his announcement and quickly looked over at Misato with a look of dread. "Misato…" _I hope he doesn't actually intend to try and cook. _

Misato caught Asuka's look of dread, understanding why she had such a look, and quickly decided to take decisive action. Knowing that Hikari was a good **cook**, she decided she could use her to help prevent the possible hazardous meal as well as having a convenient excuse for her not to be around while the commander, Asuka, and herself discussed the Shinji situation..

"Hikari, could you come over here please?" Misato requested.

Hikari nodded and slid off of the couch and onto her feet. She then made her way over to Misato.

"Could you please go help Shinji in the kitchen?" Misato asked Hikari.

"No problem Misato" Hikari said. She then made her way into the kitchen to help Shinji prepare dinner.

Misato then turned to back to Yui. "Commander, why don't we go to my room so we can discuss this matter in private" Misato suggested.

Yui nodded, "That is acceptable Major."

Asuka, Misato and Yui walked through the apartment and into Misato's thoroughly clean and organized room.

* * *

Inside the kitchen, Shinji was busy pulling out everything he needed to prepare dinner for Misato, Asuka, Hikari, his mother, and himself. After he laid everything out and began cooking the first part of the meal, Hikari walked in.

She looked around the kitchen and saw that he had everything laid out in an organized manner.

_I didn't know Shinji knew how to cook. At least, I have never seen him cook or **heard** Asuka talk about him cooking. He has everything organized by what needs to be done first._

"Hey Shinji, want some help?" Hikari asked, "Misato sent me in here."

"Sure, I guess" Shinji answered without turning around as he continued preparing dinner

Hikari asked Shinji what he was making and he told her. Hikari looked at what Shinji had already done and started on what else needed to be done. Hikari then thought to herself _I wonder why Asuka or Misato never told me that Shinji could cook._

As they cooked dinner in relative silence, Hikari built up the nerve to ask Shinji a question that had been eating away at her ever since she regained consciousness.

"Shinji, can I ask you a serious question?" Hikari asked cautiously in a soft spoken voice, uncertain if she should really ask what she wanted to.

"Sure, I guess" Shinji replied uneasily. He suspected that the question Hikari wanted to ask would make him uncomfortable and given her reaction to seeing him in his room playing his cello, he wouldn't know what to say to her.

"I don't mean to pry, but what happened? I mean with the open casket viewing and everything"

Shinji briefly stopped everything he was doing and just stood in front of the stove. Unsure of how to answer her question, Shinji decided to give the only answer he could. "I don't know what to tell you." He then resumed cooking dinner.

Seeing Shinji's delayed and noncommittal response to her question, Hikari decided not to press the issue. _Maybe he's just not at liberty to say._

The two teenagers then proceeded to finish preparing dinner.

* * *

Inside Misato's room, Asuka, Misato and Yui sat down on the floor on Misato's sleeping mat. Yui looked at both Misato and Asuka with a serious look on her face. "Now would either of you care to explain to me why Miss Horaki is here?"

Asuka looked at Misato, who gave her a reassuring glance, and swallowed nervously as she prepared to speak up. _I hope she doesn't get upset with me. _Asuka then turned her attention to the commander. "It's my fault Commander. When I arrived at school earlier today my friend Hikari quickly ran up to me after noticing my change in attire. She noticed that I seemed to be much happier than I have been for months. During the day she kept asking me what had happened that cause the change in my mood. Eventually I caved in and told her I would tell her when no one else was around. After school had ended and everyone had already left the class room, I told her that Shinji was alive. She didn't believe me and I knew the only way I could prove it to her was to bring her here."

After hearing Asuka's justification of Hikari's presence, Yui's expression softened a little but she still had a solemn expression on her face. "I can understand why you reacted the way you did, given your relationship with my son, but we can't afford to let news of Shinji being alive get out until we can come up with some sort of explanation of his presence."

Misato then decided to speak up. "That brings us to another issue. Shinji has asked about going back to school. We would need to have some sort of explanation prepared about his return and especially about the funeral and open casket viewing."

Yui nodded, "You're right. Also the explanation would have to be plausible enough for people to believe."

After several minutes of uneasy silence as they tried to come up with a plausible explanation, Asuka decided to speak up. "What about if we say that Shinji was on urgent business for NERV and had to go about it in utmost secrecy. We could say that the funeral was just a cover for him."

"Hmm. That might work, but it would still be really awkward for him to just suddenly show up after he's supposedly been dead for months." Yui commented.

"Better awkward and at school, than cooped up alone in the house all the time. Besides, people might see him anyways when he goes to NERV when the next Angel attacks" Misato added.

"Good point. So it's decided then. We will release a statement explaining Shinji's return and about both the funeral and open casket viewing" Yui stated but then paused for a moment. "On a more personal note, is it just me or is there something different about Shinji? He seems to be different from before."

_I wonder what she means by that?_ Asuka looked at over at Misato to see if she knew what the commander was talking about.

Misato nodded in response to the commander's comment and responded.

"I've definitely noticed some differences, especially after I asked him a particular question. But regardless, it's good to have him back all the same."

"Out of curiosity Misato, what did you ask Shinji this morning?" Asuka asked.

"I asked him if he remembered how he first met you Asuka."

"What did he say?"

"He said that he met you on some ship called Over the Rainbow."

"Wasn't that ship destroyed by the 6th Angel?" Asuka asked

"Yes it was. It was in a fleet from the UN that was on its way to Japan" Yui added.

"So what does this mean? Instead of just not remembering that we first met when we were really young, he has an entirely different memory all together?"

"Apparently so." Yui agreed. _This is serious. I need to speak to Dr. Akagi soon._

"In the meantimelet's not worry about how or why and just be glad that he's alive."

Each woman, all with a different but special relationship with Shinji, agreed with that statement wholeheartedly.

Asuka took in a deep breath. A delicious scent caught her attention. "Mmmm. Something smells good. Hikari must have taught Shinji how to **cook** a decent meal." _I really hope he just stayed out of her way. That way we can actually have an edible meal. I can remember that last time Shinji tried to cook for us. Terrible doesn't even begin to describe it, inedible does though._

"I don't think it will be much longer so let's go out to the dining room to wait for dinner" Asuka said, knowing her friend's excellent cooking abilities.

Both Yui and Misato nodded. All three women proceeded to get up from their positions on the sleeping mat and exit Misato's room.

* * *

As Asuka, Yui, and Misato walked back into the dining room, they saw Hikari setting the table and Shinji placing the food on the table. As soon as Shinji finished placing the food onto the table, he looked up and saw the three ladies standing by the dinner table.

"I was just about to come to tell you that dinner was ready" Shinji said.

Asuka took another deep breath. "It smells really good Shinji. Hikari must have been able to teach you a thing or two."

_I wonder what she means by that, _Shinji thought but gave her a small smile, not sure how to respond to the comment.

"Anyways, let's eat shall we?" Misato suggested.

Everyone agreed and they all sat down at the table with Asuka sitting next to Shinji of course.

A brief silence ensued as everyone began to eat their meals. "So Shinji" Yui began, breaking the silence after she swallowed the mouthful of food in her mouth, "I heard you were anxious to return to school."

"Ummm… yeah," Shinji answered after taking a sip of his soda and placing the can back down onto the table, "It's kind of boring being cooped up in the house all day."

"Depending on how fast the public relations department of NERV can work, you might be able to return to school tomorrow, thought it might be better if you waited one more day just in case. NERV needs to release a statement that will explain your reappearance after being 'dead' for several months now" Yui stated.

Shinji, though still not sure why everyone thinks he died against the fifth Angel, decided to agree anyway. "That makes sense." _Earlier Misato said she'd have to clear my return with the commander. So I guess this means my mother is the commander. But that doesn't make sense. Father has always been the commander. What exactly is going on here? There are a lot of things that are the same but then there are things that are radically different._

Not noticing her son going into deep thought, Yui continued on. "I'll give Misato a call in the morning to let her know if it is okay for you to return to school tomorrow."

Shinji, brought out of his internal monologue, just nodded. "Alright."

"About that Mrs. Ikari," Hikari interjected, "how would I explain this to our classmates and other students in the school?" _This is my chance to get an explanation about Shinji's return._

Yui turned her attention to Hikari. "Tell them while NERV regrets any grief that the funeral and open casket viewing may have caused, they were just a cover for an urgent mission for Shinji."

Hikari nodded. "Okay." _Seems kind of dubious to me, but it's still better than having no explanation._

With the most pressing issue out of the way, the dinner proceeded to be pretty normal with Asuka and Hikari talking to each other about school and gossip while Misato and Yui discussed non-classified work related materials. Shinji just listened to both conversations while eating his dinner silently hoping to gain an understanding of why so many things seemed different and yet others remained the same.

In the middle of her and Misato's conversation, Yui's cell phone rang and she told Misato to wait for a moment. The conversation between Asuka and Hikari also stopped when Yui's cell phone rang. After all, there was always the possibility that an Angel was attacking.

She left the room and she took the call. "Commander Ikari here" Yui said.

Yui listened for a little bit then answered, "Alright, meet me in my office. I'll be there shortly. Bye."

"Don't worry. It's not an Angel attack." Yui assured the group as she reentered the dining room. Hikari relaxed after hearing Yui's statement. "I just received a call from Dr. Akagi. I need to go meet her at NERV for a meeting. Regretfully, I must be leaving now."

Yui walked over to Shinji. "I would like to talk to you at NERV after school as soon as we clear your return. So please don't forget." She then gave him a hug and whispered into his ear. "I'm so glad you're back and I'm looking forward to talking to you again."

Shinji hugged his mother back and smiled as his eyes began to water up with tears again. "Me too, mother, me too. See you soon."

Shinji and Yui then released each other from their hug. "Good night everyone."

"Good night commander" Asuka and Misato said in stereo.

"Good night Mrs. Ikari."

"Good night mother." Shinji said as he cleared the tears from his eyes with his forearm.

Yui then left the dining room and made her way out of the apartment.

* * *

After the commander left, Asuka and Hikari resumed their conversation.

"Hey Hikari, this food was really good. Did Shinji help at all in the kitchen or did he just get in the way as you cooked us this excellent dinner?"

"Actually Asuka, Shinji cooked most of the dinner. I was the one helping him, not the other way around." Hikari said, "You never told me that Shinji could cook so well"

Misato and Asuka both did a spit-take and got the other's clothes wet with their drinks of choice, Asuka with Misato's beer and Misato with Asuka's favorite soda.

"What did you just say?" Misato asked incredulously. "Did you actually mention Shinji and the phrase 'cooking well' in the same sentence?"

"You obviously have never tasted his cooking before and there is a reason for that I might add" Asuka added "Calling it hazardous waste would be being polite."

Shinji felt hurt by their comments. Neither Asuka nor Misato had ever made comments like those about his cooking before. The one thing he thought he was good at, cooking, and they insult his cooking abilities _I may not be a master chef, but I know my cooking isn't as bad as Misato's cooking. Or I should say as bad what as Misato's cooking used to be. _ Shinji didn't bother waiting for anyone to say something in reply to Asuka's comment. Shinji stood up suddenly. "I'm finished." Shinji said in a soft voice with a hint of sadness that betrayed his feelings. Shinji grabbed his plate and silverware then headed to the kitchen to dump the rest of his food in the trash and then put his dishes in the sink.

After placing his dinnerware into the sink, he passed back through the dining without a word and headed towards his room.

As Shinji passed by the dining table, Asuka opened her mouth. "What's with him? It's not like his cooking has ever been good. That's why Misato usually cooks."

"That is a mean thing to say Asuka, especially after he cooked most of the dinner for us." Hikari said.

Shinji only heard Asuka's comment as he passed by the dining room table. _So that's what she meant earlier. _He then entered his room and shut the door behind him.

Misato saw Shinji's reaction and saw that the comments about his cooking had hurt Shinji's feelings. "Asuka, please drop it. Our comments seemed to have hurt Shinji" _Which is unusual since comments like those didn't usually bother him. In fact he usually **came** back with a witty reply of his own._

Now Asuka felt guilty for saying what she did. "I'll have to apologize to him later" Asuka stated. "But did he really cook this? I mean he's never cooked a meal as good as this."

"I wasn't kidding Asuka. He really did do most of the cooking."

"Hmm, he must have been practicing while he was gone" Asuka said thoughtfully, using the commander explanation's of his return to try and explain his good cooking even though she didn't really believe that statement herself.

"Even if he couldn't cook before like you said, he can certainly cook now" Hikari said.

A lull in the conversation occurred so Hikari looked at the clock on the wall **and **saw that it was getting late. "I need to be getting home Asuka. I need to finish some homework for tomorrow and get ready for bed."

"Alright, let me walk you to the door Hikari." Asuka said. Both girls got up from their chairs and walked out of the living room to the door of the apartment.

"I'm so happy for you Asuka, Shinji's back and you're not depressed anymore" Hikari said while slipping on her shoes.

"I'm glad as well. It's like a dream come true that Shinji's back. I'll be damned if I ever lose him again." Asuka said. "Just remember what the commander told you to tell anyone who asked about Shinji's return."

Hikari then gave her best friend a hug. "Just be careful. He seemed to be really hurt by the comments you and Misato made earlier."

Asuka nodded. "I will and I'll see you tomorrow in school Hikari."

"Bye Asuka. See you tomorrow."

* * *

After she watched Hikari exit the apartment and the door closed, Asuka walked back into the dining room where Misato was picking up the dirty dishes and silverware.

"Do you want some help Misato?" Asuka asked.

"No, I've got it. It's my night to do the dishes" Misato replied, "Besides don't you have an apology to make?"

Remembering what she said about Shinji's cooking earlier, Asuka felt guilty again. "Yea…." Asuka replied as she started walking towards Shinji's room.

When Asuka arrived outside of Shinji's room, she brought her right hand up to knock on the door but then paused. _How long has it been since I was in Shinji's room? How long since I could enter the room with out breaking down and crying?_

She knocked softly and called out to him. "Shinji?" She waited a few moments but got no answer. _Maybe he's asleep. I know he was upset by the comments Misato and I made but hopefully we didn't upset him too much. I should let him get some sleep. He had an emotional day today and tomorrow may be rough with everyone's reactions if he's allowed to go back to school. _

"Good night Shinji." Asuka said softly and then turned around and walked into her room to go to bed.

* * *

Shinji lay on his sleeping mat with his back to the door. He had heard Asuka knock on the door and call out his name; however he didn't feel like answering. _What did she want? Was it to insult me or my cooking some more? _Shinji thought bitterly. He hit the play button on his SDAT and he used the music to drown out Asuka knocking on the door and her calling out his name. Soon the soothing sounds of classical music lulled Shinji into a deep sleep.

* * *

Back at NERV headquarters deep in the bowels of the geofront, Yui sat at her desk in her office. Dr. Ritsuko Akagi stood at attention in front of the desk.

"So what are you trying to tell me Dr. Akagi?" Yui inquired.

"What I'm saying is that the Sea of Dirac that the 12th Angel produced could theoretically be connected to an alternate universe."

"Interesting" Yui commented with her hands crossed in front of her face. _That potentially explains his return, the reason why he doesn't know what happened to Gendo, and his response to Major Katsuragi's question. I will talk to him tomorrow after he gets out of school. Even if it turns out that he is from another universe, he is still my son. _"What is your recommendation doctor?"

"We should ask him a series of questions. We don't know how different the alternate universe may be from our own" Ritsuko stated.

"I will deal with that matter personally doctor. Yui replied. "That will be all for now doctor. Thank you."

"Yes commander." Ritsuko saluted the commander and turned to leave. _Don't let your emotions get the best of you commander. He may be your son but we still don't know how different he may be. Humanity is counting on you. We can't afford any mistakes. _ Ritsuko then left the commanders office.

After Ritsuko left her office, Yui leaned back in her chair and sighed. "Things are only going to get more complicated from here on out…."

**End Chapter 05**

* * *

. 


End file.
